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theislab / destiny

R package for single cell and other data analysis using diffusion maps
https://theislab.github.io/destiny/
GNU General Public License v3.0
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The formula of censor_value #10

Open gerrardmai opened 6 years ago

gerrardmai commented 6 years ago

Sorry for disturbing you again,

I have question for the formula of censor value showed in pdf of Diffusion -Maps.

dilutions <- read.xlsx('mmc6.xls', 1L)
dilutions$Cell <- NULL # remove annotation column
get_lod <- function(gene) gene[[max(which(gene != 28))]]

dilutions has 24 samples, If the 24th value is not equal to 28, the result will always the value of the 24th position.

whether should we find the max gene expression which is not equal to 28 (all the value in dilutions are less then 28)?

should the get_lod function be like that:

get_lod <- function(gene) gene[which(gene == max(gene[which(gene != 28)]))]
flying-sheep commented 6 years ago

i’m a bit fuzzy on the details, but basically the dilutions spreadsheet is sorted and you want to find the downmost table cell in each column that isn’t 28, therefore it’s sufficient to find the max index per column. (the only thing i don’t remember is if i just confused rows and columns)

here’s the manual, you can check if i’m right!